The Auto Scout is one of the most common enemies in FTL. It is controlled by AI and is made by the Rebels. These ships are often an easy fight in the beginning of the game, since they often lack shields. Later on, it is common for the Auto Scout to have a stealth system and highly upgraded engines, making them much tougher to damage, though they often still lack shields. Boarding is not advised on AI ships, since they don't have any oxygen in the rooms.

The Auto-Assault is slightly less common than the Auto-Scout, but nevertheless still quite common. It is more prevalent on Normal Mode than Easy Mode.
The presence of a Drone System is random, some of them have it and some don't. The Auto-Assault usually deploys anti-ship drones.
Do note that the ship is automated and can repair itself, it however cannot defend against boarding and fires. Placing a hull breach on any Auto ship prevents the ship from repairing system damage on that room. If you are using the federation cruiser type A or B while fighting this ship, using just your Artillery Beam can grant a possibility of unlocking the "Slice and Dice" achievement. (Tested)

The Elite Fighter is an uncommon Rebel ship. It will only appear in Sector 8, or when the Rebel fleet gets you. As seen on the picture, the Elite Fighter is always equipped with advanced weapons and a teleporter. A reasonable strategy is to focus on getting their deadly weapons down, before they can damage you too much.

The rebel rigger is one of the most common enemies in FTL. The Rigger will always have a drone system. It can have up to 3 drones online at the same time, allthough it will usually not have the power for a third. Damaging a system will make the Rigger reroute power to a third drone, if it has one. The rigger can use every drone in the game, except hull repair, and will use Mark.II drones later on in the game. A curious loadout for the rigger consists of a small beam weapon and a beam drone, making it impossible for said Rigger to destroy a shielded ship. If you happen to confront this ship with the Stealth Ship, the best strategy is to get out of there as fast as possible.

The triple missile launcher is probably the most dangerous weapon the flagship has, so it is advised to have cloaking and/or high evasion. Since all three missiles are fired at once, it is difficult for Defence Drones to deal with all of them.

Because the weapon rooms aren't connected to the rest of the ship, once you destroy the systems inside (and kill the crew member), they cannot be repaired. However, if you kill all the crew, an AI will take over - and damaged systems will be passively repaired. It is recommended to leave only the laser gunner alive, since he won't be able to repair the systems, will remain on the ship during all phases, will keep the AI dormant and, if you have a good enough shield and evasion, will eventually stop being a threat.

At the end of Phase 1, once you have done enough damage, the Flagship will jump away, leaving its left side behind. It therefore loses its door control, cloaking, and the triple ion.

Now that the ion weapon, cloaking, and the door control are gone, the ship redirects its power to the drones. This is arguably the hardest phase of the three.

During this phase, the Flagship will mainly focus on using drones to do damage. At the beginning of the battle, it will automatically deploy a Defence drone Mk.I, an Anti-ship drone Mk.1 and a Beam drone. It will also try to pester you with Boarding drones (about 5 in total), but having a Defence drone greatly helps with this, since it will shoot them down before they reach the ship. However, the most damage occurs when the Flagship has a power surge, swarming you with Anti-Ship drones and Beam drones. This situation can be helped by a cloaking system and high evasion. Note: destroying the ship's drone system will not prevent the drone swarm from occuring.
If you've managed to kill the ship's crew in the first phase, this phase will be much easier. At the very beginning, teleport your crew into the triple missile launcher and destroy it. After that, teleport into the drone control and proceed to destroy every other system (except the oxygen). Once you've done, take them back to your ship and deal the final blow.

When enough damage is done, the Flagship jumps away, losing is right side, including the drone control, sensors, and the beam weapon.

Having lost its right side, the ship redirects its power to a Zoltan shield and a super weapon. The battle is coming to its end.

In this phase, the Flaghip will focus on heavy lasers, but will continue to attack with its triple missile launcher and will also begin to utilize its teleporter (if it still has somebody capable of using it). When the power surge occurs, it will either fire 7 heavy laser shots at once, or regenerate the Zoltan shield. Having high evasion may not prove as useful now, but cloaking still remains a good option. As for the Zoltan shield, it will be harder to take out, due to its doubled health, but Anti-Ship drones and Ion weapons will quickly chip away at it.
The general strategy is to take out the Zoltan shield first, then destroy the missile launcher, board the ship and destroy all the systems excluding oxygen, deal the killing blow and watch the ship as it explodes.

Engi ships are a rare sight even within their own sector. They come equipped with drone systems and the Augment Engi Med-bot Dispersal. It should be noted that in later sectors, Engi ships frequently use 2 or more Defense Drones, sometimes including a Mk. II variant in the pair. As such, missiles are a poor choice against Engi ships.

Rock Assaults are a rare ship, appearing only in late game Rock sectors. They have the unique characteristic of being the only enemy ship capable of having both a teleporter and cloaking systems. As such, caution is advised when encountering one.

Early on, Slug Interceptors are easy pickings due to their lack of systems. Their oxygen and engine systems are in separate compartments, so once they're destroyed, they will not be repaired. Later on in the game, these few systems become highly upgraded, making them significantly tougher to hit. They are also the perfect ships to earn the "Victory through Asphyxiation" achievement, since their crew is incapable of repairing their oxygen supply.

All Zoltan ships (except early ones in Easy Mode) carry Zoltan Shields, allowing them to take five points of damage before their normal shields can be damaged. Missiles, Bombs and Beams will not penetrate the shield, and crew cannot teleport through them, crippling many ships that rely on those weapons early on. However, Beams and Ion weapons deal double damage to the Zoltan Shields, and drones will wear them down quickly due to their constant attacks, especially Beam Drones, which do not miss their shots.

Every type of ship except Auto-ships, Engi ships, Rock Assaults, and Crystal ships, have pirate variants. Pirate ships have randomized crew, which makes them slightly easier or tougher to board, depending on the ship class. Otherwise, they function exactly like their normal counterparts.

These crystal ships are extremely rare, generally appearing later on in the game. Their weapons are always crystal weapons, which have comparatively large cool down times and higher damage compared to most normal weapons.